García-Olivares, V;
Muñoz-Barrera, A;
Rubio-Rodríguez, LA;
Jáspez, D;
Díaz-de Usera, A;
Iñigo-Campos, A;
Veeramah, KR;
... Flores, C; + view all
(2023)
Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data.
Computational and Structural Biotechnology Journal
, 21
pp. 4613-4618.
10.1016/j.csbj.2023.09.012.
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Abstract
In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data.
| Type: | Article |
|---|---|
| Title: | Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.csbj.2023.09.012 |
| Publisher version: | https://doi.org/10.1016/j.csbj.2023.09.012 |
| Language: | English |
| Additional information: | © 2023 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology under a Creative Commons license (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Next-generation sequencing, Population genetics, NRY haplogroup classification, Comparative genomics, Y chromosome |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10178556 |
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